def prepare(self):
'''Load trajectory, print information and
perform initial alignment and fit.'''
self.load_traj()
self.atoms = self.traj.n_atoms
self.frames = self.traj.n_frames
print('\nPROTEIN INFORMATION')
print('PDB code: {}'.format(self.PDB))
print('residues: {}'.format(self.atoms))
print('frames: {}'.format(self.frames))
print('temperature: {}'.format(self.temperature))
# Align molecule to principal axes
pt.principal_axes(self.traj, dorotation=True)
# Center molecule at the origin
pt.center(self.traj, center='origin')
# First rmsd fit
pt.rmsd(self.traj)
# Calculate average structure
self.avg = pt.mean_structure(self.traj)
# Perform rms fit to average structure
pt.rmsd(self.traj, ref=self.avg)
# Initialize arrays
self.initialize_arrays()
def clean_traj(self):
# Align molecule to principal axes
pt.principal_axes(self.traj, dorotation=True)
# Center molecule at the origin
pt.center(self.traj, center='origin')
# First rmsd fit
pt.rmsd(self.traj)
# Calculate average structure
self.avg = pt.mean_structure(self.traj)
# Perform rms fit to average structure
pt.rmsd(self.traj, ref=self.avg)
def test_do_rotation(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
cm = '''
principal * dorotation mass name pout
createcrd myname
'''
state = pt.load_cpptraj_state(cm, traj)
state.run()
mut_traj_0 = traj[:]
mut_traj_1 = traj[:]
data = pt.principal_axes(mut_traj_0, mask='*', dorotation=True, mass=True)
pt.align_principal_axis(mut_traj_1, mask='*', mass=True)
aa_eq(data[0], state.data[1].values)
aa_eq(data[1], state.data[2].values)
aa_eq(state.data[-1].xyz, mut_traj_0.xyz)
aa_eq(state.data[-1].xyz, mut_traj_1.xyz)